My Latin text states that “quidquid” is an indeclinable pronoun, but doesn’t state that it is interrogative. Given the meaning “Whatever” or “Whoever”, and being so close in form to “quid” it seems logical to me that it should be treated as such.
I recently ran into a subjunctive verb in a main clause that begins with “quidquid”. Translating the clause as a jussive makes no sense, so I’m inclined to believe that “quidquid” is introducing an indirect question.
Is this correct?
Any help would be appreciated, thanks! 
Can you provide us with the sentence in question? There are a number of uses of the subjunctive (e.g. conditional sentences) in addition to those you mentioned and it’s difficult to tell you what it is in this case without knowing the context.
quidquid is definitely not indeclinable, what book are you using? (exception of the adverbial accusative)
Also, quidquid being at the beginning of the sentence does not really tell us anything about why the verb is subjunctive. Can you please provide the entire sentence, or the clause at least?